Shallow coastal embayments may play an important role in removing or retarding nutrients during their transport across the land-sea margin. These shallow sub-tidal systems generally lie within the littoral zone, have high sediment surface area to water volume ratios, and have spatially variable water residence times. Thus, benthic-pelagic coupling is especially important in regulating nutrient exchanges and transformations. The efficiency with which nutrients are retained during transport will depend upon the systemís physical and biological attributes. Rates of gross nitrogen mineralization in sediments usually exceed net rates. Mineralized nitrogen may diffuse into the overlying water column, be retained by benthic autotrophs including microalgae, seagrasses and macroalgae, or be transformed and removed by heterotrophic bacteria. Partitioning of nutrients between these fates is, in part, determined by the physical attributes of the system. We will compare nutrient cycling in shallow systems characterized by a range of residence times and in which different autotrophs dominate.